Abstract Genetic mutation and non-mutational epigenetic control of gene expression that alter transcription programs in normal and perturbed cells often lead to pathological phenotypes requiring medical attention. Identifying the gene targets and pathways underlying these abnormalities, particularly in cancer cells, is crucial for developing appropriate regimens for disease treatment. Nevertheless, the heterogeneity of cancer cells makes it difficult to develop a universal treatment plan that works for every patient. Over the past 10 years, bromodomain-containing protein 4 (BRD4) has emerged as a promising cancer therapeutic target due to its broad association with active enhancers that modulate transcription programs implicated in cancer initiation and progression, and importantly, the availability of small compound inhibitors targeting BRD4 and its related family members that also include BRD2, BRD3, and BRDT in humans. These bromodomain and extra-terminal (BET) family protein inhibitors, such as JQ1 and I-BET, show great promise in reversing cancer phenotypes in cultured cells and animal models. Several of these compound derivatives are now in clinical trials for treating various types of cancer and inflammatory disease, and their therapeutic targets have been attributed mainly to the BRD4 long isoform (BRD4-L, aa 1-1362). Recently we found, by isoform- specific knockdown and endogenous protein detection along with transgene expression, that the less abundant BRD4 short isoform (BRD4-S, aa 1-722) is in fact oncogenic while BRD4-L is tumor-suppressive in breast cancer cell proliferation and migration as well as in mammary tumor formation and metastasis. Our central hypothesis is that BRD4 isoforms have opposing functions, although they do share some common properties, in tumor development, which will be stringently tested by addressing the following three specific aims: 1. To define the biological role of BRD4-L and BRD4-S in different breast cancer cells and mouse models 2. To elucidate the mechanistic action of BRD4 isoforms and their coregulators in breast cancer subtypes 3. To identify gene targets and pathways uniquely and commonly regulated by BRD4 isoforms Since isoform-specific BRD4 antibodies and a new class of phospho-BRD4-targeting compounds with molecular action distinct from the BET bromodomain inhibitors have now been successfully developed in my lab, we are in a unique position to address pressing issues implicated in BRD4-targeted cancer therapy. Our immediate goals are to identify cellular pathways uniquely and commonly regulated by each BRD4 isoform using biochemical and molecular tools, synthetic chemistry, and genome-wide expression and binding profiling to elucidate BRD4-L and BRD4-S involvement in breast cancer. Our eventual goals are to provide validated molecular pathways and new gene targets for effective breast cancer treatment in the near future.